4V1F

Crystal structure of a mycobacterial ATP synthase rotor ring in complex with Bedaquiline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Mycobacterial ATP Synthase Fo Rotor Ring in Complex with the Anti-Tb Drug Bedaquiline.

Preiss, L.Langer, J.D.Yildiz, O.Eckhardt-Strelau, L.Guillemont, J.E.G.Koul, A.Meier, T.Preiss, L.Langer, J.D.Yildiz, O.Eckhardt-Strelau, L.Guillemont, J.E.G.Koul, A.Meier, T.

(2015) Sci.Adv. 1: 106

  • DOI: 10.1126/sciadv.1500106
  • Primary Citation of Related Structures:  4V1G

  • PubMed Abstract: 
  • Multidrug-resistant tuberculosis (MDR-TB) is more prevalent today than at any other time in human history. Bedaquiline (BDQ), a novel Mycobacterium-specific adenosine triphosphate (ATP) synthase inhibitor, is the first drug in the last 40 years to be ...

    Multidrug-resistant tuberculosis (MDR-TB) is more prevalent today than at any other time in human history. Bedaquiline (BDQ), a novel Mycobacterium-specific adenosine triphosphate (ATP) synthase inhibitor, is the first drug in the last 40 years to be approved for the treatment of MDR-TB. This bactericidal compound targets the membrane-embedded rotor (c-ring) of the mycobacterial ATP synthase, a key metabolic enzyme required for ATP generation. We report the x-ray crystal structures of a mycobacterial c9 ring without and with BDQ bound at 1.55- and 1.7-Å resolution, respectively. The structures and supporting functional assays reveal how BDQ specifically interacts with the rotor ring via numerous interactions and thereby completely covers the c-ring's ion-binding sites. This prevents the rotor ring from acting as an ion shuttle and stalls ATP synthase operation. The structures explain how diarylquinoline chemicals specifically inhibit the mycobacterial ATP synthase and thus enable structure-based drug design of next-generation ATP synthase inhibitors against Mycobacterium tuberculosis and other bacterial pathogens.


    Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F0F1 ATP SYNTHASE SUBUNIT C
A, B, C
86N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BQ1
Query on BQ1

Download SDF File 
Download CCD File 
A, B, C
Bedaquiline
C32 H31 Br N2 O2
QUIJNHUBAXPXFS-XLJNKUFUSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
B, C
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.156 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 75.048α = 90.00
b = 75.048β = 90.00
c = 166.550γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references